Shanks and Joplin (RNCSE 2000; 20 [1–2]: 25–30) disputed Michael Behe's irreducible complexity challenge to evolution, arguing that there was at least one way for evolutionary change to accomplish this task. Their article prompted a response from Michael Behe, and a reply from Shanks and Joplin.

In their article "Of mousetraps and men: Behe on biochemistry" (RNCSE 2000; 20 [1–2]: 25–30), which has just come to my attention, Shanks and Joplin appear mistakenly to attribute to me the contention that irreducibly complex biochemical systems must have been created ex nihilo. I have never claimed that. I have no reason to think that a designer could not have used suitably modified pre-existent material. My argument in Darwin's Black Box was directed merely toward the conclusion of design. How the design was effected is a separate and much more difficult question to address. Although creation ex nihilo is a formal possibility, design might have been produced by some other means that involved no discontinuities in natural law, even if the designer is a supernatural being.

One possibility is directed mutations. As noted by Brown University biologist Kenneth Miller in Finding Darwin's God (New York: HarperCollins, 1999), "[t]he indeterminate nature of quantum events would allow a clever and subtle God to influence events in ways that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations..." (p 241). I have no reason to object to that as a route to irreducibly complex systems. I would just note further that such a process amounts to "intelligent design", and that while we may be unable to discern the means by which the design is effected, the resultant design itself may be detected in the structure of the irreducibly complex system.

The core claim of intelligent design theory is quite limited. It says nothing directly about how biological design was produced, who the designer was, whether there has been common descent, or other such questions. Those can be addressed separately. It says only that design can be empirically detected in observable features of physical systems. As an important corollary, it also predicts that mindless processes such as natural selection or the self-organization scenarios favored by Shanks and Joplin will not be demonstrated to be able to produce irreducible systems of the complexity found in cells.